# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 20:36:08 2022
#   Inital geometry file: a 90 line input string
#   Ligand name: (2S,3S)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-2,3-dihydro-4H-chromen-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@@H](Oc2cc(O)cc(O)c2C1=O)c3ccc(O)c(O)c3
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 DH2  DH2  (2S,3S)-2-(3,4-dihydroxyphenyl)-3,5,7-trihydroxy-2,3-dihydro-4H-chromen-4-one  ligand  34  22  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_DH2
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 DH2  C1   C  CR16  0  -0.506  -0.7180   0.2244  -4.4705
 DH2  C2   C  CR6   0   0.412   0.4450  -0.0122  -3.7573
 DH2  C3   C  CR66  0  -0.338   0.4364   0.0164  -2.3414
 DH2  C4   C  CR66  0   0.440  -0.7698   0.3260  -1.6817
 DH2  C5   C  CR16  0  -0.482  -1.9321   0.5652  -2.3836
 DH2  C6   C  CR6   0   0.411  -1.8969   0.4987  -3.7791
 DH2  C9   C  CR6   0   0.395   1.6075  -0.3266  -1.5819
 DH2  C10  C  CR16  0  -0.049   1.4144  -0.4503  -0.0829
 DH2  C11  C  CR16  0  -0.074   0.3896   0.5861   0.3714
 DH2  C14  C  CR6   0   0.109   0.0870   0.4946   1.8356
 DH2  C15  C  CR16  0  -0.332   0.5142   1.4888   2.6990
 DH2  C16  C  CR16  0  -0.360   0.2656   1.3880   4.0637
 DH2  C17  C  CR6   0   0.250  -0.4179   0.2970   4.5707
 DH2  C18  C  CR6   0   0.311  -0.8591  -0.7124   3.7002
 DH2  C19  C  CR16  0  -0.383  -0.6008  -0.6063   2.3456
 DH2  O12  O  O     0  -0.477  -0.8310   0.3929  -0.3435
 DH2  O13  O  O     0  -0.459   2.7031  -0.5585  -2.0882
 DH2  O23  O  OH1   0  -0.634  -1.5311  -1.7900   4.1552
 DH2  O24  O  OH1   0  -0.641  -0.7081   0.1203   5.8779
 DH2  O27  O  OH1   0  -0.650   2.5912  -0.2373   0.6272
 DH2  O29  O  OH1   0  -0.612  -3.0448   0.7280  -4.4185
 DH2  O30  O  OH1   0  -0.619   1.5599  -0.2794  -4.4265
 DH2  H1   H  HCR6  0   0.286  -0.7011   0.1942  -5.5534
 DH2  HB   H  HCR6  0   0.281  -2.8512   0.8083  -1.8670
 DH2  HD   H  HCR6  0   0.262   0.9973  -1.4577   0.0924
 DH2  H11  H  HCR6  0   0.277   0.7805   1.5859   0.1399
 DH2  H15  H  HCR6  0   0.258   1.0413   2.3540   2.3175
 DH2  H16  H  HCR6  0   0.277   0.6051   2.1699   4.7331
 DH2  H19  H  HCR6  0   0.263  -0.9507  -1.3977   1.6925
 DH2  H23  H  HOH1  0   0.473  -1.6693  -1.7271   5.1076
 DH2  H24  H  HOH1  0   0.484  -0.3694   0.8496   6.4085
 DH2  H27  H  HOH1  0   0.462   3.2871  -0.7801   0.2393
 DH2  HC   H  HOH1  0   0.485  -2.9269   0.6621  -5.3737
 DH2  HA   H  HOH1  0   0.479   2.2834  -0.4263  -3.7791

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 DH2  C1   C2   aromatic  1.385  0.020  1.385
 DH2  C1   C6   aromatic  1.394  0.020  1.394
 DH2  C1   H1   single    0.930  0.020  1.080
 DH2  C2   C3   aromatic  1.416  0.020  1.416
 DH2  C2   O30  single    1.327  0.020  1.327
 DH2  C3   C4   aromatic  1.409  0.020  1.409
 DH2  C3   C9   single    1.437  0.020  1.437
 DH2  C4   C5   aromatic  1.379  0.020  1.379
 DH2  C4   O12  single    1.341  0.020  1.341
 DH2  C5   C6   aromatic  1.397  0.020  1.397
 DH2  C5   HB   single    0.930  0.020  1.080
 DH2  C6   O29  single    1.334  0.020  1.334
 DH2  C9   C10  single    1.516  0.020  1.516
 DH2  C9   O13  double    1.229  0.020  1.229
 DH2  C10  C11  single    1.527  0.020  1.527
 DH2  C10  O27  single    1.391  0.020  1.391
 DH2  C10  HD   single    0.970  0.020  1.090
 DH2  C11  C14  single    1.498  0.020  1.498
 DH2  C11  O12  single    1.428  0.020  1.428
 DH2  C11  H11  single    0.970  0.020  1.090
 DH2  C14  C15  aromatic  1.384  0.020  1.384
 DH2  C14  C19  aromatic  1.395  0.020  1.395
 DH2  C15  C16  aromatic  1.391  0.020  1.391
 DH2  C15  H15  single    0.930  0.020  1.080
 DH2  C16  C17  aromatic  1.384  0.020  1.384
 DH2  C16  H16  single    0.930  0.020  1.080
 DH2  C17  C18  aromatic  1.404  0.020  1.404
 DH2  C17  O24  single    1.351  0.020  1.351
 DH2  C18  C19  aromatic  1.383  0.020  1.383
 DH2  C18  O23  single    1.349  0.020  1.349
 DH2  C19  H19  single    0.930  0.020  1.080
 DH2  O23  H23  single    0.850  0.020  0.980
 DH2  O24  H24  single    0.850  0.020  0.980
 DH2  O27  H27  single    0.850  0.020  0.980
 DH2  O29  HC   single    0.850  0.020  0.980
 DH2  O30  HA   single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 DH2  H1   C1   C6   120.96  3.000
 DH2  H1   C1   C2   119.80  3.000
 DH2  C6   C1   C2   119.24  3.000
 DH2  O30  C2   C3   120.88  3.000
 DH2  O30  C2   C1   118.70  3.000
 DH2  C3   C2   C1   120.42  3.000
 DH2  C9   C3   C4   120.16  3.000
 DH2  C9   C3   C2   121.23  3.000
 DH2  C4   C3   C2   118.53  3.000
 DH2  O12  C4   C5   117.45  3.000
 DH2  O12  C4   C3   121.13  3.000
 DH2  C5   C4   C3   121.42  3.000
 DH2  HB   C5   C6   120.59  3.000
 DH2  HB   C5   C4   120.80  3.000
 DH2  C6   C5   C4   118.62  3.000
 DH2  O29  C6   C5   116.67  3.000
 DH2  O29  C6   C1   121.59  3.000
 DH2  C5   C6   C1   121.73  3.000
 DH2  O13  C9   C10  120.35  3.000
 DH2  O13  C9   C3   123.62  3.000
 DH2  C10  C9   C3   115.98  3.000
 DH2  HD   C10  O27  112.23  3.000
 DH2  HD   C10  C11  108.57  3.000
 DH2  O27  C10  C11  108.19  3.000
 DH2  HD   C10  C9   106.22  3.000
 DH2  O27  C10  C9   112.61  3.000
 DH2  C11  C10  C9   108.92  3.000
 DH2  H11  C11  O12  108.78  3.000
 DH2  H11  C11  C14  109.48  3.000
 DH2  O12  C11  C14  107.97  3.000
 DH2  H11  C11  C10  108.44  3.000
 DH2  O12  C11  C10  109.46  3.000
 DH2  C14  C11  C10  112.64  3.000
 DH2  C19  C14  C15  119.41  3.000
 DH2  C19  C14  C11  120.35  3.000
 DH2  C15  C14  C11  120.23  3.000
 DH2  H15  C15  C16  119.39  3.000
 DH2  H15  C15  C14  120.29  3.000
 DH2  C16  C15  C14  120.31  3.000
 DH2  H16  C16  C17  119.82  3.000
 DH2  H16  C16  C15  119.85  3.000
 DH2  C17  C16  C15  120.33  3.000
 DH2  O24  C17  C18  116.01  3.000
 DH2  O24  C17  C16  124.33  3.000
 DH2  C18  C17  C16  119.66  3.000
 DH2  O23  C18  C19  119.00  3.000
 DH2  O23  C18  C17  121.44  3.000
 DH2  C19  C18  C17  119.56  3.000
 DH2  H19  C19  C18  118.27  3.000
 DH2  H19  C19  C14  121.01  3.000
 DH2  C18  C19  C14  120.72  3.000
 DH2  C11  O12  C4   117.86  3.000
 DH2  H23  O23  C18  110.63  3.000
 DH2  H24  O24  C17  111.01  3.000
 DH2  H27  O27  C10  108.61  3.000
 DH2  HC   O29  C6   110.96  3.000
 DH2  HA   O30  C2   108.46  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 DH2  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 DH2  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 DH2  CONST_03  C5   C6   C1   C2      0.00   0.0  0
 DH2  CONST_04  C5   C4   C3   C2      0.00   0.0  0
 DH2  CONST_05  C6   C1   C2   C3      0.00   0.0  0
 DH2  CONST_06  C6   C5   C4   C3      0.00   0.0  0
 DH2  CONST_07  C17  C16  C15  C14     0.00   0.0  0
 DH2  CONST_08  C17  C18  C19  C14     0.00   0.0  0
 DH2  CONST_09  C18  C19  C14  C15     0.00   0.0  0
 DH2  CONST_10  C18  C17  C16  C15     0.00   0.0  0
 DH2  CONST_11  C19  C14  C15  C16     0.00   0.0  0
 DH2  CONST_12  C19  C18  C17  C16     0.00   0.0  0
 DH2  CONST_13  C16  C15  C14  C11   180.00   0.0  0
 DH2  CONST_14  C18  C19  C14  C11   180.00   0.0  0
 DH2  CONST_15  O29  C6   C1   C2    180.00   0.0  0
 DH2  CONST_16  O30  C2   C3   C4    180.00   0.0  0
 DH2  CONST_17  O29  C6   C5   C4    180.00   0.0  0
 DH2  CONST_18  O30  C2   C1   C6    180.00   0.0  0
 DH2  CONST_19  O30  C2   C3   C9      0.00   0.0  0
 DH2  CONST_20  O23  C18  C19  C14   180.00   0.0  0
 DH2  CONST_21  O24  C17  C16  C15   180.00   0.0  0
 DH2  CONST_22  O23  C18  C17  C16   180.00   0.0  0
 DH2  CONST_23  O24  C17  C18  C19   180.00   0.0  0
 DH2  CONST_24  HB   C5   C6   C1    180.00   0.0  0
 DH2  CONST_25  H1   C1   C2   C3    180.00   0.0  0
 DH2  CONST_26  H15  C15  C14  C11     0.00   0.0  0
 DH2  CONST_27  H19  C19  C14  C11     0.00   0.0  0
 DH2  CONST_28  H16  C16  C15  C14   180.00   0.0  0
 DH2  Var_01    C10  C9   C3   C2   -171.52  30.0  1

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 DH2  chir_01  C10  C9   C11  O27  positiv
 DH2  chir_02  C11  O12  C10  C14  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 DH2  plan-1  C11  0.020
 DH2  plan-1  C14  0.020
 DH2  plan-1  C15  0.020
 DH2  plan-1  C16  0.020
 DH2  plan-1  C17  0.020
 DH2  plan-1  C18  0.020
 DH2  plan-1  C19  0.020
 DH2  plan-1  O23  0.020
 DH2  plan-1  O24  0.020
 DH2  plan-1  H15  0.020
 DH2  plan-1  H16  0.020
 DH2  plan-1  H19  0.020
 DH2  plan-2  C1   0.020
 DH2  plan-2  C2   0.020
 DH2  plan-2  C3   0.020
 DH2  plan-2  C4   0.020
 DH2  plan-2  C5   0.020
 DH2  plan-2  C6   0.020
 DH2  plan-2  C9   0.020
 DH2  plan-2  O12  0.020
 DH2  plan-2  O29  0.020
 DH2  plan-2  O30  0.020
 DH2  plan-2  H1   0.020
 DH2  plan-2  HB   0.020
 DH2  plan-3  C3   0.020
 DH2  plan-3  C9   0.020
 DH2  plan-3  C10  0.020
 DH2  plan-3  O13  0.020

